High shear mixer granulators are typically found in pharmaceutical and detergent industries, and are capable of reducing processing time and producing agglomerates with high strength and density. Generally, several granulation scaling-up stages are involved before reaching the production level. This is conducted to exert better understanding, control and optimization at the smaller scales before proceeding to the larger scales in terms of geometric, kinematic and/or dynamic similarities. During granulation scaling-up stages, the mechanics of particle interactions and the prevailing level of compressive stresses and strains within the granulator are affected by the variation in hydrodynamics of the granulator as a result of different scales. This in turn affects the final structure of the agglomerates. In this paper we analyze the effect of velocity field of two different scales of high shear mixer granulator (1 and 5 1) on the structure of the evolved agglomerates. The study is based on computer simulation using the discrete element method (DEM). A single agglomerate is generated using DEM computer code and is placed in a bed of primary particles. A velocity field is then superimposed on the surrounding particles. This velocity field corresponds to that obtained experimentally from a separate study using Positron Emission Particle Tracking analysis on 1-and 5-1 granulators which were scaled up based on the condition of constant shear stress. The results show that when the velocity profile of the 1-1 granulator is used the agglomerate becomes more elongated and it has a smaller packing fraction. Therefore the agglomerate would be weaker.